How does the government count the fish?

Fishermen unloaded and weighed cod in Gloucester. John Tlumacki/Globe Staff

There are a lot of fish in the sea. How to count them? It is, surprisingly, one of the hottest questions in New England public life these days.

Massachusetts Governor-elect Charlie Baker, concerned about sharp restrictions on cod fishing in the Gulf of Maine, has openly questioned whether the federal government is accurately tallying the iconic species.

“My continued concern about this,” he said recently, “is there’s only one source of truth.”

And aggrieved fishermen, an iconic species of their own, have argued that the abundant catch in their nets this year belies the government’s warnings of a species on the brink of collapse.

Scientists and environmentalists have offered broad rebuttals to Baker and the fishermen in the news media, often blaming the problem on decades of overfishing. But there has been little detailed discussion of how the federal government actually counts fish and how reliable its numbers are.

The decades-old count, it turns out, is a sprawling effort, overseen by the National Oceanic and Atmospheric Administration’s Northeast Fisheries Science Center, based in Woods Hole.

Observers on fishermen’s boats track what they are catching and where. Analysts pore over catch data filed by dealers at the dock. And samplers at ports inspect a fish ear structure known as the otolith whose calcified rings reveal the age of a fish — just as tree rings show the age of a tree.

Age is important. Scientists say information on how a particular cohort of fish is faring — 1-year-old summer flounder or 5-year-old cod — says something critical about the long-term health of the population.

The federal government gleans this sort of information not just from the commercial catch, but from a catch of its own. And it is a NOAA boat called the Henry B. Bigelow that trawls for the fish.

The 208-foot vessel, named after the oceanographer who founded the Woods Hole Oceanographic Institution in 1931, conducts two surveys in the Gulf of Maine yearly, one in the spring and one in the fall.

A computer program dispatches the Bigelow to 50 to 70 randomly selected spots in the gulf to conduct 20-minute drags with a large net known as an “otter trawl,” held open by steel panels and plastic floats.

The net grabs dozens of species of sea life, which scientists weigh, measure, and slice open to determine the fishes’ sex and where they are in the spawning process.

All the data go into a complex statistical model. And every few months, NOAA produces a thick, peer-reviewed assessment of one of the species the agency studies — such as Atlantic striped bass, white hake, or cod.

The latest cod assessment, released last month, was stark. It found the species has dwindled to between 3 and 4 percent of what it would take to sustain a healthy population. And last week, federal officials responded with what amounted to a six-month ban on cod fishing in the gulf.

This week, the New England Fishery Management Council took a big step toward more permanent reductions on cod, slashing already puny annual catch limits by 75 percent for the next fishing season, which starts in May.

Gloucester fisherman Al Cottone, who has been on the water full-time for 31 years, said the cuts don’t match up with what fishermen have found in the gulf this year — a bumper crop of cod. And part of the problem, he said, is that the Bigelow is not going where the fish are.

“They pick random spots,” he said. “And where they’re going, there are no fishermen there. What does that tell you?”

Most scientists dismiss the argument. They say cod congregate. Finding their gathering points, they said, is a sign of a good fisherman, not a healthy stock.

But Steven Cadrin, an associate professor of fisheries oceanography at the University of Massachusetts Dartmouth, said NOAA would benefit from more data collected aboard fishermen’s boats — and more data in general.

Conducting a watery census over 20,255 square miles on a limited budget is no easy endeavor, observers said.

And with less-than-trustworthy numbers, Cadrin argued, the government is ill-equipped to make fine-tuned decisions on how many metric tons of a given fish — 200? 500? — the fishing fleet should be able to pull from the water per year.

“I think in the context of this uncertainty, it’s very safe to say that more information and more investment would help produce better science for management of fisheries,” Cadrin said.

Chris Legault, supervisory research fisheries biologist at NOAA’s Northeast Fisheries, acknowledged that it is difficult to make small-scale adjustments in catch limits with confidence. But the system is quite adept, he said, at distinguishing between the need for a catch limit of, say, 500 metric tons or 5,000.

“I think we need to keep in perspective that all models are saying the catch for the Gulf of Maine cod has to be very, very low,” he said.

Indeed, there is a broad consensus in the scientific community that, whatever the quibbles with this or that snapshot of where a fish population stands, consistent findings of decline in a long-studied species such as cod are nearly unimpeachable.

“Where we gain our strength,” Legault said, “is doing this over time.”

If anything, NOAA scientists said, retrospective analyses have found them consistently overestimating the size of the Gulf of Maine cod stock.

Why the cod the population continues to decline, even in the face of stricter and stricter fishing quotas, is a bit of a mystery. Thomas A. Nies, executive director of the New England Fishery Management Council, said some chalk up the mortality to a growing seal population, others to a warming ocean.

“The cod are being parboiled,” he said, summing up the climate change argument. “They vote with their fins, so they’ve left.”

But Mike Palmer, a research fisheries biologist with Northeast Fisheries, said the evidence for these theories is circumstantial.

Seals, for instance, eat plenty of haddock, and the haddock stock is surging.

The most likely explanation, he said: Repeated overestimates of the cod stock have led to too-high catch quotas, year after year.

Overfishing, he argued, is the real culprit.